PDBsum entry 1r5c

Hydrolase

PDB id: 1r5c

Contents

Protein chains

124 a.a. *

Ligands

CPA ×2

Waters ×91

* Residue conservation analysis

PDB id:

1r5c

Name:

Hydrolase

Title:

X-ray structure of the complex of bovine seminal ribonuclease swapping dimer with d(cpa)

Structure:

Ribonuclease, seminal. Chain: a, b. Synonym: seminal rnase, s-rnase, ribonuclease bs-1. Ec: 3.1.27.5

Source:

Bos taurus. Cattle. Organism_taxid: 9913

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.190 R-free: 0.242

Authors:

A.Merlino,L.Vitagliano,F.Sica,A.Zagari,L.Mazzarella

Key ref:

A.Merlino et al. (2004). Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer. Biopolymers, 73, 689-695. PubMed id: 15048772

Date:

10-Oct-03 Release date: 13-Apr-04

Protein chains

P00669  (RNS_BOVIN) -  Seminal ribonuclease from Bos taurus

Seq: 150 a.a.

Struc: 124 a.a.

Enzyme reactions

• Enzyme class: E.C.4.6.1.18 - pancreatic ribonuclease.
• Reaction:
  1. an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
  2. an [RNA] containing uridine + H2O = an [RNA]-3'-uridine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]

Biopolymers 73:689-695 (2004)

PubMed id: 15048772

Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer.

A.Merlino, L.Vitagliano, F.Sica, A.Zagari, L.Mazzarella.

ABSTRACT

Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. This enzyme exists as two conformational isomers with distinctive biological properties. The structure of the major isomer is characterized by the swapping of the N-terminal segment (MxM BS-RNase). In this article, the crystal structures of the ligand-free MxM BS-RNase and its complex with 2'-deoxycitidylyl(3',5')-2'-deoxyadenosine derived from isomorphous crystals have been refined. Interestingly, the comparison between this novel ligand-free form and the previously published sulfate-bound structure reveals significant differences. In particular, the ligand-free MxM BS-RNase is closer to the structure of MxM BS-RNase productive complexes than to the sulfate-bound form. These results reveal that MxM BS-RNase presents a remarkable flexibility, despite the structural constraints of the interchain disulfide bridges and the swapping of the N-terminal helices. These findings have important implications to the ligand binding mechanism of MxM BS-RNase. Indeed, a population shift rather than a substrate-induced conformational transition may occur in the MxM BS-RNase ligand binding process.